Commit graph

13196 commits

Author SHA1 Message Date
Shintaro Iwasaki
71cd91e4c1 update Argobots and BOLT (#13765)
* argobots: update to 1.0rc2

* bolt: update to 1.0rc3

* argobots/bolt: add maintainers

* argobots: use "master" for the master branch
2019-11-20 19:04:46 -07:00
Douglas Duckworth
100fcc2c8e added hmmer v 3.3 (#13793) 2019-11-20 19:04:27 -07:00
Brian Van Essen
2f069b571d Updated versions numbers for Aluminum and Hydrogen. (#13814) 2019-11-20 19:04:01 -07:00
Paul Ferrell
fb3a3ba95e mirror bug fixes: symlinks, duplicate patch names, and exception handling (#13789)
* Some packages (e.g. mpfr at the time of this patch) can have patches
  with the same name but different contents (which apply to different
  versions of the package). This appends part of the patch hash to the
  cache file name to avoid conflicts.
* Some exceptions which occur during fetching are not a subclass of
  SpackError and therefore do not have a 'message' attribute. This
  updates the logic for mirroring a single spec (add_single_spec)
  to produce an appropriate error message in that case (where before
  it failed with an AttributeError)
* In various circumstances, a mirror can contain the universal storage
  path but not a cosmetic symlink; in this case it would not generate
  a symlink. Now "spack mirror create" will create a symlink for any
  package that doesn't have one.
2019-11-20 17:00:44 -07:00
t-karatsu
9cd778f152 ampliconnoise: Change return type of function. (#13766)
* ampliconnoise: Change function type.

* ampliconnoise: updated api call to setup run environment
2019-11-20 16:03:51 -07:00
健美猞猁
1e52aa750a find-circ: a new package. (#13767)
* find-circ: a new package.

* flake8.
2019-11-20 16:02:34 -07:00
健美猞猁
5e9ca0f939 miranda: a new package. (#13768) 2019-11-20 16:01:41 -07:00
Figroc Chen
ace47cecbe tensorflow-serving-client: add new package (#13771) 2019-11-20 16:01:04 -07:00
t-karatsu
af9281b843 bpp-suite: Clarify 'isinf' function's namespace. (#13777) 2019-11-20 15:52:44 -07:00
David Hows
ad4986be94 Fix for overlong shebang in valgrind (#13779)
Fix for some overlong shebangs in valgrind. Borrowed from verrou/package.py
2019-11-20 15:50:14 -07:00
noguchi-k
894267e02e py-numexpr3: fix version (#13781) 2019-11-20 15:49:13 -07:00
Ken Raffenetti
f25cf16b11 mpich: Add 3.3.2 (#13790) 2019-11-20 15:48:11 -07:00
Justin S
63874db562 genrich: new package at 0.6 (#13791) 2019-11-20 15:47:36 -07:00
Justin S
38ae7ab6cd sentieon-genomics: add 201808.07 (#13794) 2019-11-20 15:46:22 -07:00
Adam J. Stewart
4e4e3d192e
Add old version of py-gast (#13806) 2019-11-20 15:21:03 -07:00
Adam J. Stewart
0d1e9c6e06
Add py-google-pasta package (#13807) 2019-11-20 15:20:47 -07:00
Adam J. Stewart
d43364d679
Add new py-grpcio package (#13808) 2019-11-20 15:20:28 -07:00
Adam J. Stewart
d19eb21181
Add c-ares 1.15.0 (#13809) 2019-11-20 15:20:08 -07:00
Adam J. Stewart
33059daff4
Add old versions and missing dependencies to py-protobuf (#13811) 2019-11-20 15:19:47 -07:00
Adam J. Stewart
ea42d67a9a
Add old version of jdk (#13805)
* Add old version of jdk

* setup_environment -> setup_build_environment
2019-11-20 15:19:22 -07:00
Brian Van Essen
66cf530459 Added package for Clara command line parser (#13763)
* Added package for Clara command line parser
2019-11-20 00:12:43 -07:00
t-karatsu
513fe55fc3 Features/expand microarch for aarch64 (#13780)
* Add process to determine aarch64 microarchitecture

* add microarchitectures for thunderx2 and a64fx

* Add optimize flags for gcc on aarch64 family processors thunderx2 and a64fx.

* Add optimize flags for clang on aarch64 family processors thunderx2 and a64fx

* Add testing for thunderx2 and a64fx microarchitectures
2019-11-20 00:01:12 -07:00
albestro
f25a4ab089 add MAX_CPU_COUNT variant to HPX package (#13769)
* add MAX_CPU_COUNT variant to HPX package

* compatibility with python2

* correct variant description

Co-Authored-By: Mikael Simberg <mikael.simberg@iki.fi>

* add maintainers list
2019-11-19 12:49:32 -07:00
George Hartzell
d00be588e3 zlib: use setup_build_environment for build env (#13786)
zlib was using the deprecated setup_environment call.  Now it's using
the current setup_build_environment.

(noticed this in some `spack -d` output)
2019-11-19 12:29:35 -07:00
ktsai7
bb0667ceaf add more legion version and expose more flecsi options (#13741)
* add more legion version and expose more flecsi options

* formatting

* update version pointing to master to master

* fix indentation

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* use self.run_tests

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2019-11-18 23:51:41 -07:00
Greg Becker
99dfff4475
binary distribution: relocate text files properly in relative binaries (#13578)
* Make relative binaries relocate text files properly
* rb strings aren't valid in python 2
* move perl to new interface for setup_environment family methods
2019-11-18 14:13:42 -07:00
健美猞猁
e433a5dc0b py-rnacocktail: a new package. (#13761)
* py-rnacocktail: a new package.

* flake8.

* Add build-time dependencies.
2019-11-18 14:09:39 -07:00
albestro
e0746a2a07 fix libxml2 url (#13770)
http to https
2019-11-18 10:58:16 -07:00
Xavier Delaruelle
e5b3202352 environment-modules: add version 4.4.0 (#13772) 2019-11-18 10:53:06 -07:00
Massimiliano Culpo
ab62ad463d
py-xattr: fix a package that was pointing to a fork (#13685)
The package now points to the official github repository for master
and to PyPI for release versions.
2019-11-18 12:09:47 +01:00
oracleLee
686e613e94 Update scalpel package.py (#13746)
* Update package.py

Update scalpel version 0.5.4

* Update package.py
2019-11-17 12:45:16 -07:00
Cyrus Harrison
d3c1547dba update to add ascent 0.5.0 release (#13709)
* fix metis src dl url

* update ascent, vtk-h and vtk-m recipes

* update conduit package

* fix vtk-m shas

* mfem conduit fix

* use vtk-h develop

* fix issue with stripped include paths in mfem

* more metis fixes

* simpler fix for mfem conduit include issue

* finish mfem changes

* pin to cmake 3.14, since we hit cuda issues with 3.15

* add rtd theme as dep for ascent

* add vtk-h 0.5.0 release, update ascent to use it

* add ascent 0.5.0 release

* fix cmake pin to allow all vers of 3.14

* fix format string error in mfem pkg

* review fixes for mfem pkg

* review fixes for vtk-h and vtk-m packages

* address review comments for ascent pkg

* changing default off of develop broke downstream use

* revert prefed
2019-11-17 12:36:14 -07:00
Axel Huebl
02f27fc45d openPMD-api: 0.10.0 (#13750)
Add latest release and first to be tagged by number in Spack,
version 0.10.0.
2019-11-17 12:35:40 -07:00
Hector Martinez-Seara
15207bae43 guile package: Handling the threads option. (#13730)
* guile package: Handling the threads option.

Currently guile by default tries to compile its thread variant.
However, the threaded version can only be compiled if bdw-gc is
compiled with some threads support. Currently, the default
compilation of the bdw garbage collector is compiled without any
thread support resulting in a compilation error.

I have changed the the default guile compilation to the non-threaded
version. I have also added the appropiated options for the bdw-gc
compilation in case the user prefers the threaded variant.

* guile package(flake8): fixed identation issues
2019-11-16 14:34:38 -07:00
Nick Booher
c8c8dca5b5 revbayes: add new versions (#13760) 2019-11-16 00:12:38 -07:00
Tim Fuller
3dbafb5ee7 Fix for issue #13754 (#13755)
* remove reference to `spack.store` in method definition

Referencing `spack.store` in method definition will cache the `spack.config.config` singleton variable too early, before we have a chance to add command line and environment scopes.
2019-11-15 13:32:58 -08:00
Adam J. Stewart
5510bba1fd
Document use of the maintainers field (#12270)
* Document use of the maintainers field

* Use fake GitHub usernames

* GitHub action is not automatic yet
2019-11-15 13:58:24 -06:00
Greg Becker
c587c76537 Config option to allow gpg warning suppression (#13743)
Add a configuration option to suppress gpg warnings during binary
package verification. This only suppresses warnings: a gpg failure
will still fail the install. This allows users who have already
explicitly trusted the gpg key they are using to avoid seeing
repeated warnings that it is self-signed.
2019-11-14 16:22:01 -08:00
Satish Balay
40c77bf158
xsdk@0.5.0 (#13682)
Update:
 hypre@2.18.2
 mfem@4.0.1-xsdk
 superlu-dist@6.1.1
 trilinos@12.18.1
 - dtk-3.1
 petsc@3.12.1
 dealii@9.1.1
 pflotran@xsdk-0.5.0
 alquimia@xsdk-0.5.0
 sundials@5.0.0
 plasma@19.8.1
 magma@2.5.1
 amrex@19.08
 slepc@3.12.0
 omega-h@9.29.0
 strumpack@3.3.0
 pumi@2.2.1
 tasmanian@7.0
 phist@1.8.0

New:
 ginkgo@1.1.0
 py-libensemble@0.5.2
 precice@1.6.1
 butterflypack@1.1.0

Add variants:
 ginkgo
 libensemble
 precice
 butterflypack
 strumpack
 trilinos

tasmanian:  use ~openmp only on OSX
precice: disable on OSX
enable sundials+superlu-dist
sundials+superlu-dist requires OpenMP 4.5+ (so enable only for gcc@6.1+)
enable mfem+sundials
enable sundials+petsc+superlu_dist
remove hypre~internal-superlu
petsc: build with +batch on cray
precice: use ~petsc on cray
libensemble: add as runtime dependency for PYTHONPATH
2019-11-14 16:36:51 -06:00
t-karatsu
94c9e5f9a0 z3: bugfix about python dependency and fallthrough annotation. (#13713)
* z3:

* Fixed python dependency to always be required.

* bugfix about fallthrough annotation.

* z3: Add patch for before ver.4.4.1.

* Update var/spack/repos/builtin/packages/z3/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-14 16:28:05 -06:00
Seth R. Johnson
e670476024 Mark conflicts between newer packages and Intel 14 compilers (#13729)
* Mark compiler/version conflict for CMake

Intel 14 lacks some C++11 features needed to compile new versions of
cmake.
```
/tmp/s3j/spack-stage/spack-stage-cmake-3.15.5-46lgp4ybhopy2p4rr66rxnew5iaddvmg/spack-src/Source/
cm_static_string_view.hxx(28): error: expected an operator
   friend static_string_view operator"" _s(const char* data, size_t
                                     ^
```

* Mark compiler/version conflict for icu4c

With Intel 14.0.4 on Linux for icu4c 60.1 and higher:
```
locid.cpp(1156): error #1140: a using-declaration may not name a constructor or destructor
        using KeywordEnumeration::KeywordEnumeration;
```

* Mark compiler/version conflict for nasm

Error installing `nasm@2.14.02%intel@14.0.4`:
```
In file included from nasmlib/crc64.c(35):
./include/nasmlib.h(116): error: expected a ";"
  fatal_func nasm_assert_failed(const char *, int, const char *);
```

* Mark compiler/version conflict for bison

Installing `bison@3.4.2%intel@14.0.4`:
```
In file included from /tmp/s3j/spack-stage/spack-stage-bison-3.4.2-
uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/quotearg.c(33):
/tmp/s3j/spack-stage/spack-stage-bison-3.4.2-uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/
xalloc.h(51): warning #303: explicit type is missing ("int" assumed)
  extern _Noreturn void xalloc_die (void);
```

* Mark compiler/version conflict for icu4c

With `icu4c@60.1%intel@16.0.4` and `icu4c@64.1%intel@16.0.4`:

```
In file included from ucurr.cpp(26):
static_unicode_sets.h(130): error #913: invalid multibyte character sequence
      {POUND_SIGN, u'£'},
                     ^
```

* Change conflict comments into messages
2019-11-14 16:27:36 -06:00
George Hartzell
7a6c7f23a0 py-matplotlib only needs backports when ^python@:2 (#13712)
* py-matplotlib only needs backports when ^python@:2

This implements @scheibelp's suggestion in #13711.

py-matplotlib should only depends_on py-backports-functools-lru-cache
when it's using a python that actually *needs* it.

See #13711 for details.

* Don't depend_ons py-enum34 unless python@:3.3

* Tighten up enum34 dependency

@adamjstewart cracked open the setup.py files and suggested a tighter
dependency for py-enum34.  1.4 and 1.5 only require it for pythons
before 3.4, 1.3 requires it unconditionally.  So...., we'll do the
same.

* Remove conflict on python 3.4 from enum34

at @adamjstewart's request see PR notes
2019-11-14 16:26:44 -06:00
Gregory Lee
8490587c76 add boost dependency to stat package (#13735) 2019-11-14 16:26:24 -06:00
xfzhao
2fb5df0284 update to v0.6.4 (#13737) 2019-11-14 16:26:08 -06:00
Emir İşman
46871416b1 Update DMTCP package to v2.6.0 (#13739) 2019-11-14 16:20:44 -06:00
Nicholas Sly
d79d11b6d4 Removed github repository and develop version from dataspaces package as it is no longer present/accessible. (#13740) 2019-11-14 16:20:13 -06:00
xfzhao
11e65661ac update vsearch (#13736) 2019-11-14 16:17:02 -06:00
Massimiliano Culpo
7e84fe966c hwloc: added 'master' version pointing at the HEAD of the master branch (#13731) 2019-11-14 12:06:07 -06:00
Sinan
00bf299e46 new package Qscintilla (with python bindings via py-pyqt ) (#12793)
* qscintilla_with_python_bindings_disabled

* pyqt5 with variant +qsci to compile qscintilla python bindings

* fix a dyn linking issue for Qsci python module

* fix a bug

* fix bug: use sip provided by py-pyqt5

* fix typo

* tidy up, make designer

* tidy up

* fix designer build issue, set env for designer plugin

* tidy up

* tidy up

* minor improvements

* improve style

* build Qscintilla python bindings here

* make qsci config option variant dependent

* get rid of commented out code

* improvements: add resource for qscintilla, improve config_args

* flake8: spaces, blank lines etc

* flake8: fix long lines

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* dont install source tree under prefix

* remove duplicate line

* use os.path.join instead of +

* separate build and run environment setups

* flake8

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* fix rsrc path

* use python_include_dir

* use "with working_dir"

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* flake8
2019-11-14 12:01:49 -06:00
Matthias Maiterth
ab2b3f30a5 package/geopm: Added versions 1.0.0 and 1.1.0 (#13721)
* package/geopm: Added versions 1.0.0 and 1.1.0

Added changes for 1.1.0 and 1.0.0 in this patch.
Patch for 1.0.0 was previously not merged.
variant for hwloc removed since that is not a dependency since 0.5.1 and
variant('hwloc', when=:0.5.1 is not supported afaik.
made depends_on versions more explicit.

* package/geopm: removed 1.0.0 release candidates 1 and 2.
2019-11-14 12:01:03 -06:00